@article{Holland2008,
	title = {{BioJava}: an open-source framework for bioinformatics},
	volume = {24},
	issn = {1460-2059},
	url = {http://dx.doi.org/10.1093/bioinformatics/btn397},
	doi = {10.1093/bioinformatics/btn397},
	abstract = {Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.},
	number = {18},
	journal = {Bioinformatics},
	author = {Holland, R. C. G. and Down, T. A. and Pocock, M. and Prlić, A. and Huen, D. and James, K. and Foisy, S. and Dräger, A. and Yates, A. and Heuer, M. and Schreiber, M. J.},
	month = sep,
	year = {2008},
	pmid = {18689808},
	keywords = {bioinformatics, java},
	pages = {2096--2097}
}

@article{zenodo,
	Author = {Willighagen, Egon},
	Doi = {10.5281/zenodo.4400601},
	Month = {Jul},
	Publisher = {Zenodo},
	Title = {{egonw/bacting: Bacting 0.0.15}},
	Year = {2020}
}

@article{bioclipse1,
	title = {Bioclipse: an open source workbench for chemo- and bioinformatics},
	volume = {8},
	copyright = {All rights reserved},
	issn = {1471-2105},
	url = {http://dx.doi.org/10.1186/1471-2105-8-59},
	doi = {10.1186/1471-2105-8-59},
	abstract = {There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework.},
	number = {1},
	journal = {BMC Bioinformatics},
	author = {Spjuth, Ola and Helmus, Tobias and Willighagen, Egon L. and Kuhn, Stefan and Eklund, Martin and Wagener, Johannes and Murray-Rust, Peter and Steinbeck, Christoph and Wikberg, Jarl E.},
	month = feb,
	year = {2007},
	pmcid = {PMC1808478},
	pmid = {17316423},
	keywords = {bioclipse, bioinformatics, cheminformatics, collabcheminf, eclipse, java, licenseepl, opensource, papers, richclient},
	pages = {59+}
}

@article{bioclipse2,
	title = {Bioclipse 2: {A} scriptable integration platform for the life sciences},
	volume = {10},
	copyright = {All rights reserved},
	issn = {1471-2105},
	shorttitle = {Bioclipse 2},
	url = {http://www.biomedcentral.com/1471-2105/10/397},
	doi = {10.1186/1471-2105-10-397},
	language = {en},
	number = {1},
	urldate = {2017-11-16},
	journal = {BMC Bioinformatics},
	author = {Spjuth, Ola and Alvarsson, Jonathan and Berg, Arvid and Eklund, Martin and Kuhn, Stefan and Mäsak, Carl and Torrance, Gilleain and Wagener, Johannes and Willighagen, Egon L and Steinbeck, Christoph and Wikberg, Jarl ES},
	year = {2009},
	keywords = {bioclipse, bioinformatics, cheminformatics, collabcheminf, eclipse, java, licenseepl, papers, richclient},
	pages = {397}
}

@article{Willighagen2017,
	title = {The {Chemistry} {Development} {Kit} ({CDK}) v2.0: atom typing, depiction, molecular formulas, and substructure searching},
	volume = {9},
	copyright = {All rights reserved},
	issn = {1758-2946},
	shorttitle = {The {Chemistry} {Development} {Kit} ({CDK}) v2.0},
	url = {http://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4},
	doi = {10.1186/s13321-017-0220-4},
	language = {en},
	number = {1},
	urldate = {2017-11-16},
	journal = {Journal of Cheminformatics},
	author = {Willighagen, Egon L. and Mayfield, John W. and Alvarsson, Jonathan and Berg, Arvid and Carlsson, Lars and Jeliazkova, Nina and Kuhn, Stefan and Pluskal, Tomáš and Rojas-Chertó, Miquel and Spjuth, Ola and Torrance, Gilleain and Evelo, Chris T. and Guha, Rajarshi and Steinbeck, Christoph},
	month = dec,
	year = {2017}
}

@article{Lowe2011,
	title = {Chemical name to structure: {OPSIN}, an open source solution.},
	volume = {51},
	issn = {1549-960X},
	url = {http://dx.doi.org/10.1021/ci100384d},
	doi = {10.1021/ci100384d},
	abstract = {We have produced an open source, freely available, algorithm (Open Parser for Systematic IUPAC Nomenclature, OPSIN) that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using an approach based on a regular grammar. This grammar is used to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an XML parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. Results from OPSIN on various computer generated name/structure pair sets are presented. These show exceptionally high precision (99.8\%+) and, when using general organic chemical nomenclature, high recall (98.7-99.2\%). This software can serve as the basis for future open source developments of chemical name interpretation.},
	number = {3},
	journal = {Journal of Chemical Information and Modeling},
	author = {Lowe, Daniel M. and Corbett, Peter T. and Murray-Rust, Peter and Glen, Robert C.},
	month = mar,
	year = {2011},
	pmid = {21384929},
	keywords = {cdk–usespackage–renderer, cdk–usespackage–smiles, cheminformatics, iupac},
	pages = {739--753}
}

@article{vanIersel2010,
	title = {The {BridgeDb} framework: standardized access to gene, protein and metabolite identifier mapping services},
	volume = {11},
	issn = {1471-2105},
	url = {http://dx.doi.org/10.1186/1471-2105-11-5},
	doi = {10.1186/1471-2105-11-5},
	abstract = {Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.},
	number = {1},
	journal = {BMC Bioinformatics},
	author = {van Iersel, Martijn P. and Pico, Alexander R. and Kelder, Thomas and Gao, Jianjiong and Ho, Isaac and Hanspers, Kristina and Conklin, Bruce R. and Evelo, Chris T.},
	month = jan,
	year = {2010},
	pmid = {20047655},
	keywords = {access, bridgedb, framework, geneprotein, identifier, mapping, metabolite, services, standardised},
	pages = {5+}
}

@article{Spjuth2013,
	title = {Applications of the {InChI} in cheminformatics with the {CDK} and {Bioclipse}},
	volume = {5},
	copyright = {All rights reserved},
	issn = {1758-2946},
	url = {http://jcheminf.springeropen.com/articles/10.1186/1758-2946-5-14},
	doi = {10.1186/1758-2946-5-14},
	language = {en},
	number = {1},
	urldate = {2017-11-16},
	journal = {Journal of Cheminformatics},
	author = {Spjuth, Ola and Berg, Arvid and Adams, Samuel and Willighagen, Egon L},
	year = {2013},
	keywords = {cdk–useslibrary},
	pages = {14}
}

@article{vanRijswijk2017,
	title = {The future of metabolomics in {ELIXIR}},
	volume = {6},
	copyright = {All rights reserved},
	issn = {2046-1402},
	url = {https://f1000research.com/articles/6-1649/v1},
	doi = {10.12688/f1000research.12342.1},
	language = {en},
	urldate = {2017-11-16},
	journal = {F1000Research},
	author = {van Rijswijk, Merlijn and Beirnaert, Charlie and Caron, Christophe and Cascante, Marta and Dominguez, Victoria and Dunn, Warwick B. and Ebbels, Timothy M. D. and Giacomoni, Franck and Gonzalez-Beltran, Alejandra and Hankemeier, Thomas and Haug, Kenneth and Izquierdo-Garcia, Jose L. and Jimenez, Rafael C. and Jourdan, Fabien and Kale, Namrata and Klapa, Maria I. and Kohlbacher, Oliver and Koort, Kairi and Kultima, Kim and Le Corguillé, Gildas and Moschonas, Nicholas K. and Neumann, Steffen and O’Donovan, Claire and Reczko, Martin and Rocca-Serra, Philippe and Rosato, Antonio and Salek, Reza M. and Sansone, Susanna-Assunta and Satagopam, Venkata and Schober, Daniel and Shimmo, Ruth and Spicer, Rachel A. and Spjuth, Ola and Thévenot, Etienne A. and Viant, Mark R. and Weber, Ralf J. M. and Willighagen, Egon L. and Zanetti, Gianluigi and Steinbeck, Christoph},
	month = sep,
	year = {2017},
	pages = {1649}
}

@article{Slenter2018,
	title = {{WikiPathways}: a multifaceted pathway database bridging metabolomics to other omics research},
	volume = {46},
	copyright = {All rights reserved},
	issn = {0305-1048, 1362-4962},
	shorttitle = {{WikiPathways}},
	url = {http://academic.oup.com/nar/article/doi/10.1093/nar/gkx1064/4612963},
	doi = {10.1093/nar/gkx1064},
	language = {en},
	number = {D1},
	urldate = {2017-11-16},
	journal = {Nucleic Acids Research},
	author = {Slenter, Denise N. and Kutmon, Martina and Hanspers, Kristina and Riutta, Anders and Windsor, Jacob and Nunes, Nuno and Mélius, Jonathan and Cirillo, Elisa and Coort, Susan L. and Digles, Daniela and Ehrhart, Friederike and Giesbertz, Pieter and Kalafati, Marianthi and Martens, Marvin and Miller, Ryan and Nishida, Kozo and Rieswijk, Linda and Waagmeester, Andra and Eijssen, Lars M.T. and Evelo, Chris T. and Pico, Alexander R. and Willighagen, Egon L.},
	month = jan,
	year = {2018},
	keywords = {WikiPathways},
	pages = {D661--D667}
}

@article{Willighagen2018,
	title = {Wikidata and {Scholia} as a hub linking chemical knowledge},
	copyright = {CC BY 4.0},
	url = {https://figshare.com/articles/Wikidata_and_Scholia_as_a_hub_linking_chemical_knowledge/6356027/1},
	doi = {10.6084/m9.figshare.6356027.v1},
	abstract = {Poster presented at the 11th International Conference on Chemical Structures, May 27-31 2018, Noordwijkerhout, The Netherlands.},
	urldate = {2019-08-25},
	journal = {Figshare},
	author = {Willighagen, Egon and Slenter, Denise and Mietchen, Daniel and Evelo, Chris and Nielsen, Finn},
	year = {2018},
	keywords = {Cheminformatics}
}

@inbook{Nielsen2017,
	title = {Scholia, {Scientometrics} and {Wikidata}},
	volume = {10577},
	isbn = {978-3-319-70406-7 978-3-319-70407-4},
	url = {http://link.springer.com/10.1007/978-3-319-70407-4_36},
	urldate = {2020-07-19},
	booktitle = {The {Semantic} {Web}: {ESWC} 2017 {Satellite} {Events}},
	publisher = {Springer International Publishing},
	author = {Nielsen, Finn Årup and Mietchen, Daniel and Willighagen, Egon},
	editor = {Blomqvist, Eva and Hose, Katja and Paulheim, Heiko and Ławrynowicz, Agnieszka and Ciravegna, Fabio and Hartig, Olaf},
	year = {2017},
	doi = {10.1007/978-3-319-70407-4_36},
	note = {Series Title: Lecture Notes in Computer Science},
	pages = {237--259}
}

@article{Mayfield2019,
	title = {cdk/cdk: {CDK} 2.3},
	copyright = {Open Access},
	shorttitle = {cdk/cdk},
	url = {https://zenodo.org/record/3364510},
	abstract = {The Chemistry Development Kit},
	urldate = {2020-07-19},
	publisher = {Zenodo},
	author = {Mayfield, John and Willighagen, Egon and Rajarshi Guha and Gilleain Torrance and Ujihara, Kazuya and Rahman, Syed Asad and Alvarsson, Jonathan and Vine, Mark B and Gražulis, Saulius and Tomáš Pluskal and Yap Chun Wei and Szisz, Daniel and Williamson, Mark J. and Kochev, Nikolay and Jeliazkova, Nina and Bach, Eric and Berg, Arvid and Clark, Alex and Stephan, Ralf and Wenk, Michael and Ficolas2 and Stueker, Oliver and Dole, Krishna and Jönsson, Klas and Kaibioinfo and Burgoon, Lyle and Katsubo, Dmitry and AndyHowlettGitHub and Köhler, Uli and Harmon, Cyrus},
	month = aug,
	year = {2019},
	doi = {10.5281/ZENODO.3364510}
}

@article{Brenninkmeijer2020,
	title = {bridgedb/{BridgeDb}: {BridgeDb} 2.3.8},
	copyright = {Open Access},
	shorttitle = {bridgedb/{BridgeDb}},
	url = {https://zenodo.org/record/3855084},
	urldate = {2020-07-19},
	publisher = {Zenodo},
	author = {Brenninkmeijer, Christian Y. and Willighagen, Egon and Awasthi, Manas and Soiland-Reyes, Stian and Riutta, Anders and Pico, Alexander and Dunlop, Ian and Nunogit and Kerber, Randy and De and MyGrid Jenkins Build Server and Summer-Kutmon, Martina and Mélius, Jonathan and Martens, Marvin and Gray, Alasdair and Ehrhart, Friederike},
	month = may,
	year = {2020},
	doi = {10.5281/ZENODO.3855084}
}

@article{Afantitis2020,
	title = {{NanoSolveIT} {Project}: {Driving} {Nanoinformatics} research to develop innovative and integrated tools for in silico nanosafety assessment},
	copyright = {All rights reserved},
	issn = {20010370},
	shorttitle = {{NanoSolveIT} {Project}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2001037019305112},
	doi = {10.1016/j.csbj.2020.02.023},
	language = {en},
	urldate = {2020-03-08},
	journal = {Computational and Structural Biotechnology Journal},
	author = {Afantitis, Antreas and Melagraki, Georgia and Isigonis, Panagiotis and Tsoumanis, Andreas and Danai Varsou, Dimitra and Valsami-Jones, Eugenia and Papadiamantis, Anastasios and Ellis, Laura-Jayne.A and Sarimveis, Haralambos and Doganis, Philip and Karatzas, Pantelis and Tsiros, Periklis and Liampa, Irene and Lobaskin, Vladimir and Greco, Dario and Serra, Angela and Anneli Sofia Kinaret, Pia and Aliisa Saarimäki, Laura and Grafström, Roland and Kohonen, Pekka and Nymark, Penny and Willighagen, Egon and Puzyn, Tomasz and Rybinska-Fryca, Anna and Lyubartsev, Alexander and Alstrup Jensen, Keld and Gerit Brandenburg, Jan and Lofts, Stephen and Svendsen, Claus and Harrison, Samuel and Maier, Dieter and Tamm, Kaido and Jänes, Jaak and Sikk, Lauri and Dusinska, Maria and Longhin, Eleonora and Rundén-Pran, Elise and Mariussen, Espen and El Yamani, Naouale and Unger, Wolfgang and Radnik, Jörg and Tropsha, Alexander and Cohen, Yoram and Leszczynski, Jerzy and Ogilvie Hendren, Christine and Wiesner, Mark and Winkler, David and Suzuki, Noriyuki and Hyun Yoon, Tae and Choi, Jang-Sik and Sanabria, Natasha and Gulumian, Mary and Lynch, Iseult},
	month = mar,
	year = {2020},
	pages = {S2001037019305112}
}

@misc{Willighagen2020,
	title = {Metabolite {BridgeDb} {ID} {Mapping} {Database} (20200610)},
	copyright = {CC0},
	url = {https://figshare.com/articles/Metabolite_BridgeDb_ID_Mapping_Database_20200610_/12458612},
	abstract = {BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of April 2020), ChEBI 186 (Release of April 2020), and Wikidata (10 June 2020) as data sources.},
	urldate = {2020-07-19},
	publisher = {figshare},
	author = {Willighagen, Egon},
	year = {2020},
	doi = {10.6084/M9.FIGSHARE.12458612},
	keywords = {Cheminformatics, 60102 Bioinformatics, FOS: Computer and information sciences}
}

@article{Hastings2015,
	title = {{eNanoMapper}: harnessing ontologies to enable data integration for nanomaterial risk assessment},
	volume = {6},
	copyright = {All rights reserved},
	issn = {2041-1480},
	shorttitle = {{eNanoMapper}},
	url = {http://www.jbiomedsem.com/content/6/1/10},
	doi = {10.1186/s13326-015-0005-5},
	language = {en},
	number = {1},
	urldate = {2017-11-16},
	journal = {Journal of Biomedical Semantics},
	author = {Hastings, Janna and Jeliazkova, Nina and Owen, Gareth and Tsiliki, Georgia and Munteanu, Cristian R and Steinbeck, Christoph and Willighagen, Egon},
	month = dec,
	year = {2015},
	keywords = {enanomapper, ontology, owl}
}

